Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008785.1 Hibiscus syriacus cultivar Beakdansim tig00111917_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1341157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:196972 original size:105 final size:105
Alignment explanation
Indices: 196817--197114 Score: 551
Period size: 105 Copynumber: 2.8 Consensus size: 105
196807 AAATTATTTA
* * *
196817 TTGACAACCAGTGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTTTGGAGTCCAATATCCTTCG
1 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
196882 TTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
*
196922 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
196987 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
197027 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
197092 TTGTGAAGTTGAAATTGGCTCTG
66 TTGTGAAGTTGAAATTGGCTCTG
197115 GGTAAAACCT
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 187 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
Found at i:197891 original size:21 final size:21
Alignment explanation
Indices: 197863--197906 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
197853 ACCCACCTTA
197863 TTTTCTCTTATT-TTGTTCTT
1 TTTTCTCTTATTCTTGTTCTT
* *
197883 TTTTCCTCTTTTTCTTTTTCTT
1 TTTT-CTCTTATTCTTGTTCTT
197905 TT
1 TT
197907 CTCAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTCTTATTCTTGTTCTT
Found at i:197986 original size:63 final size:66
Alignment explanation
Indices: 197883--198005 Score: 162
Period size: 63 Copynumber: 1.9 Consensus size: 66
197873 TTTTGTTCTT
* * * *
197883 TTTTCCTCTTTTTCTTTTTCTTTTCTCAATTTAGGGCGCCCTTTCGGGGTTTCACCCTAAATGTT
1 TTTTCCTCTTCTTCTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGGTTTCACCCTAAATGTT
197948 C
66 C
* * *
197949 TTTTCTTCTTCTTC-TTTT-TTTT-TCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTCCTCTTCTTCTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGGTTTCACCCTAA
198006 GCGAAGTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 30 0.60
64 4 0.08
65 4 0.08
66 12 0.24
ACGTcount: A:0.11, C:0.26, G:0.12, T:0.50
Consensus pattern (66 bp):
TTTTCCTCTTCTTCTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGGTTTCACCCTAAATGTT
C
Found at i:204592 original size:20 final size:21
Alignment explanation
Indices: 204559--204599 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
204549 TGATCTTCTA
*
204559 ATATTTTTATCTTT-TCTTCC
1 ATATTTTTAGCTTTATCTTCC
*
204579 ATATTTTTGGCTTTATCTTCC
1 ATATTTTTAGCTTTATCTTCC
204600 TCATCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.61
Consensus pattern (21 bp):
ATATTTTTAGCTTTATCTTCC
Found at i:208478 original size:9 final size:9
Alignment explanation
Indices: 208466--208523 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
208456 AGAAAATAAG
208466 TAAATAAAA
1 TAAATAAAA
208475 TAAATAAAA
1 TAAATAAAA
208484 T--ATAAAA
1 TAAATAAAA
*
208491 -AAACAAGAA
1 TAAATAA-AA
*
208500 -AAATGAAA
1 TAAATAAAA
208508 TAAAT-AAA
1 TAAATAAAA
208516 TAAATAAA
1 TAAATAAA
208524 GTATGAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
7 6 0.15
8 13 0.32
9 22 0.54
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (9 bp):
TAAATAAAA
Found at i:208479 original size:4 final size:4
Alignment explanation
Indices: 208459--208523 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
208449 GTAATAAAGA
* * * * *
208459 AAAT AAGT AAAT AAAAT AAAT AAA- ATAT AAAA AAAC AAGAA AAAT GAAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT
208509 AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAA
208524 GTATGAGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 2 0.04
4 36 0.73
5 11 0.22
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:208613 original size:32 final size:33
Alignment explanation
Indices: 208551--208617 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
208541 TAAATAATAT
*
208551 ATATATATATATGAAATGATGATATAAAAAAGTG
1 ATATATATATATGAAATGATGACATAAAAAA-TG
208585 ATATATATATAT-AAAT-ATGTACAT-AAAAATG
1 ATATATATATATGAAATGATG-ACATAAAAAATG
208616 AT
1 AT
208618 GAAGCATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 4 0.13
32 8 0.26
33 7 0.23
34 12 0.39
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (33 bp):
ATATATATATATGAAATGATGACATAAAAAATG
Found at i:208644 original size:2 final size:2
Alignment explanation
Indices: 208637--208663 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
208627 AGTATTATGA
208637 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
208664 AAATAGCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:209179 original size:20 final size:20
Alignment explanation
Indices: 209154--209192 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
209144 CTGCCTCGCC
*
209154 GCCGCCGTTGAACGGCGACG
1 GCCGCCGTTCAACGGCGACG
*
209174 GCCGCCGTTCATCGGCGAC
1 GCCGCCGTTCAACGGCGAC
209193 AAAATCACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.36, T:0.13
Consensus pattern (20 bp):
GCCGCCGTTCAACGGCGACG
Found at i:214623 original size:55 final size:55
Alignment explanation
Indices: 214223--214606 Score: 572
Period size: 55 Copynumber: 7.0 Consensus size: 55
214213 ATTACCAAAT
* * * *
214223 GGCACTGTGTGTGCAAAAATTAAGAAATTCATAATGAGTTTATGAATTTTCATATG
1 GGCACTTTGTGTGC-AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * *
214279 GGCACTTTGTGTGCAAAACTAATAAATTCATAATGAGTATATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
214334 GGCATTTTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
** * *
214389 AACACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * *
214444 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAG-TTATGAATTTCCGTATA
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
214498 GGCACTTTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATAAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
214553 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTATATGAATTTCCGTAT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
214607 TGGTAGTGGG
Statistics
Matches: 297, Mismatches: 30, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
54 50 0.17
55 234 0.79
56 13 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (55 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
Found at i:214623 original size:164 final size:165
Alignment explanation
Indices: 214223--214602 Score: 609
Period size: 164 Copynumber: 2.3 Consensus size: 165
214213 ATTACCAAAT
* * * *
214223 GGCACTGTGTGTGCAAAAATTAAGAAATTCATAATGAGTTTATGAATTTTCATATGGGCACTTTG
1 GGCACTTTGTGTGC-AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTG
* * * *
214288 TGTGCAAAACTAATAAATTCATAATGAGTATATGAATTTTCGTATGGGCATTTTATGTGCAAAAC
65 TGTGCAAAACTAAGAAATTCATAATGAGTATATGAATTTCCGTATAGGCACTTTATGTGCAAAAC
*
214353 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
130 TAAGAAATTCATAATAAGTTTATAAATTTTCGTATG
** *
214389 AACACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTGT
* *
214454 GTGCAAAACTAAGAAATTCATAATGAGT-TATGAATTTCCGTATAGGCACTTTGTGTGTAAAACT
66 GTGCAAAACTAAGAAATTCATAATGAGTATATGAATTTCCGTATAGGCACTTTATGTGCAAAACT
214518 AAGAAATTCATAATAAGTTTATAAATTTTCGTATG
131 AAGAAATTCATAATAAGTTTATAAATTTTCGTATG
*
214553 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTATATGAATTTCC
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCC
214603 GTATTGGTAG
Statistics
Matches: 197, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
164 112 0.57
165 74 0.38
166 11 0.06
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (165 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTGT
GTGCAAAACTAAGAAATTCATAATGAGTATATGAATTTCCGTATAGGCACTTTATGTGCAAAACT
AAGAAATTCATAATAAGTTTATAAATTTTCGTATG
Found at i:220148 original size:20 final size:19
Alignment explanation
Indices: 220121--220181 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
220111 CATTTTGGTG
220121 CAGAGGGAATCGATACCCC
1 CAGAGGGAATCGATACCCC
* * *
220140 CATGAGGGAACCCATTCCCCC
1 CA-GAGGGAATCGA-TACCCC
*
220161 CACAGGGGAATCGATACCCC
1 CAGA-GGGAATCGATACCCC
220181 C
1 C
220182 TGGGGTTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.50
21 14 0.44
ACGTcount: A:0.28, C:0.38, G:0.23, T:0.11
Consensus pattern (19 bp):
CAGAGGGAATCGATACCCC
Found at i:220180 original size:21 final size:21
Alignment explanation
Indices: 220122--220181 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
220112 ATTTTGGTGC
220122 AGAGGGAATCGATA-CCCCCA
1 AGAGGGAATCGATACCCCCCA
* * * *
220142 TGAGGGAACCCATTCCCCCCA
1 AGAGGGAATCGATACCCCCCA
220163 CAG-GGGAATCGATACCCCC
1 -AGAGGGAATCGATACCCCC
220182 TGGGGTTCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 10 0.33
21 19 0.63
22 1 0.03
ACGTcount: A:0.28, C:0.37, G:0.23, T:0.12
Consensus pattern (21 bp):
AGAGGGAATCGATACCCCCCA
Found at i:229463 original size:20 final size:22
Alignment explanation
Indices: 229421--229468 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
229411 ACTGTAATGG
*
229421 AGTATCGGTATCATAGGATAGA
1 AGTATCGGTATCATAGGAGAGA
229443 AGTATCGGTA-C-TAGGAGAGA
1 AGTATCGGTATCATAGGAGAGA
*
229463 AATATC
1 AGTATC
229469 AATACCATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 1 0.04
22 10 0.42
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (22 bp):
AGTATCGGTATCATAGGAGAGA
Found at i:229474 original size:94 final size:94
Alignment explanation
Indices: 229351--229542 Score: 269
Period size: 94 Copynumber: 2.0 Consensus size: 94
229341 AGCTGAACAA
* * * * *
229351 TATCGATACTATGGAGAAAGTATCGATACCATTGATTCAGAATGTAGAAATGGTATCGATACTGT
1 TATCGATACTATGGAGAAAATATCAATACCATGGATCCAGAATGTAGAAATGGTATCGATACTGA
* * *
229416 AATGGAGTATCGGTATCATAGGATAGAAG
66 AAGGGAGTATCGGTACCACAGGATAGAAG
* *
229445 TATCGGTACTA-GGAGAGAAATATCAATACCATGGATCCATAATGTAGAAATGGTATCGATACTG
1 TATCGATACTATGGAGA-AAATATCAATACCATGGATCCAGAATGTAGAAATGGTATCGATACTG
*
229509 AAAGGGAGTATCGGTACCACAGTATAGAAG
65 AAAGGGAGTATCGGTACCACAGGATAGAAG
229539 TATC
1 TATC
229543 AATAGTTGCT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 5 0.06
94 81 0.94
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (94 bp):
TATCGATACTATGGAGAAAATATCAATACCATGGATCCAGAATGTAGAAATGGTATCGATACTGA
AAGGGAGTATCGGTACCACAGGATAGAAG
Found at i:230398 original size:55 final size:55
Alignment explanation
Indices: 229889--230381 Score: 815
Period size: 55 Copynumber: 8.9 Consensus size: 55
229879 GACCAAATGA
*
229889 CACTGTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
1 CACTTTGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* *
229945 CACTTTGTATGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGCATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * *
230000 CACTTTGTGTGAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGAG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* *
230055 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
230110 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
230165 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
*
230220 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * ** **
230275 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATAAATTTTTGTATAAG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * *
230330 CACATTGTGTGCAAAACTAAGAAATTCATAATAAGTATATGAATTTCCGTAT
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
230382 TGGTAGTGGG
Statistics
Matches: 411, Mismatches: 26, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
55 401 0.98
56 10 0.02
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (55 bp):
CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
Found at i:232069 original size:39 final size:38
Alignment explanation
Indices: 232000--232155 Score: 161
Period size: 39 Copynumber: 4.0 Consensus size: 38
231990 CACTCATTTT
* * * *
232000 ACCTCAACCTTGGGCATTACCAGCC-TTATTGAACTGATCC
1 ACCTC-ACCTTAGGCATTATC-GCCTTTATTGCACTCA-CC
* * *
232040 ACCTCACTTTAGGCGTTATCGCCTTTATTGCACTCAACA
1 ACCTCACCTTAGGCATTATCGCCTTTATTGCACTC-ACC
* *
232079 ACCTCACCTTAGGCATTATCACCTTTATTGCACTCAAC
1 ACCTCACCTTAGGCATTATCGCCTTTATTGCACTCACC
* *
232117 ATCCTCACCTTAGGCATTATCGTCTTTATTACACTCACC
1 A-CCTCACCTTAGGCATTATCGCCTTTATTGCACTCACC
232156 TAATAATGAC
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
38 5 0.05
39 86 0.89
40 6 0.06
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.32
Consensus pattern (38 bp):
ACCTCACCTTAGGCATTATCGCCTTTATTGCACTCACC
Found at i:232107 original size:78 final size:79
Alignment explanation
Indices: 232000--232153 Score: 188
Period size: 78 Copynumber: 2.0 Consensus size: 79
231990 CACTCATTTT
* * * * *
232000 ACCTCAACCTTGGGCATTACCAGCCTTATTGAACTGATCCA-CCTCACTTTAGGCGTTATCGCCT
1 ACCTCAACCTTAGGCATTACCAGCCTTATTGAACTCA-ACATCCTCACCTTAGGCATTATCGCCT
*
232064 TTATTGCACTCAACA
65 TTATTACACTCAACA
* * *
232079 ACCTC-ACCTTAGGCATTATCA-CCTTTATTGCACTCAACATCCTCACCTTAGGCATTATCGTCT
1 ACCTCAACCTTAGGCATTACCAGCC-TTATTGAACTCAACATCCTCACCTTAGGCATTATCGCCT
232142 TTATTACACTCA
65 TTATTACACTCA
232154 CCTAATAATG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
77 4 0.06
78 55 0.86
79 5 0.08
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.32
Consensus pattern (79 bp):
ACCTCAACCTTAGGCATTACCAGCCTTATTGAACTCAACATCCTCACCTTAGGCATTATCGCCTT
TATTACACTCAACA
Found at i:237693 original size:13 final size:13
Alignment explanation
Indices: 237675--237726 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
237665 GTAACCCATT
237675 TTTATTTATTTAA
1 TTTATTTATTTAA
237688 TTTATTTTTATTTAA
1 TTTA--TTTATTTAA
* *
237703 TTT-TAGTATTTGA
1 TTTAT-TTATTTAA
237716 TTTATTTATTT
1 TTTATTTATTT
237727 TGATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 1 0.03
13 18 0.56
14 1 0.03
15 12 0.38
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTATTTATTTAA
Found at i:237712 original size:19 final size:19
Alignment explanation
Indices: 237672--237723 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
237662 GAGGTAACCC
*
237672 ATTTTTATTTATTTAATTT
1 ATTTTTATTTATTTAATGT
*
237691 ATTTTTATTTAATTTTA-GT
1 ATTTTTATTT-ATTTAATGT
*
237710 A-TTTGATTTATTTA
1 ATTTTTATTTATTTA
237724 TTTTGATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 12 0.43
20 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
ATTTTTATTTATTTAATGT
Found at i:249285 original size:31 final size:32
Alignment explanation
Indices: 249249--249319 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
249239 TTAGAACAAC
* *
249249 TAATATGTAT-TATATGAAATGAGTTACAAAA
1 TAATATATATATATATGAAATAAGTTACAAAA
249280 TAATATATATATATATGAAATAAGTTACAAAA
1 TAATATATATATATATGAAATAAGTTACAAAA
249312 TAACTATA
1 TAA-TATA
249320 ACTAGATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 9 0.25
32 23 0.64
33 4 0.11
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (32 bp):
TAATATATATATATATGAAATAAGTTACAAAA
Found at i:264898 original size:36 final size:35
Alignment explanation
Indices: 264816--264905 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 35
264806 TAAACAAGGT
264816 ATAAAAAATAATAGTAATAATAAGTACTAAAATAA
1 ATAAAAAATAATAGTAATAATAAGTACTAAAATAA
264851 A-AATAATAATAATAGTAATAAATAAAGTA-T-AAATGAA
1 ATAA-AA-AATAATAGTAAT-AAT-AAGTACTAAAAT-AA
*
264888 ATAAAAAATAATAATAAT
1 ATAAAAAATAATAGTAAT
264906 GGAAATATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
34 2 0.04
35 3 0.06
36 27 0.56
37 9 0.19
38 7 0.15
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.27
Consensus pattern (35 bp):
ATAAAAAATAATAGTAATAATAAGTACTAAAATAA
Found at i:266533 original size:99 final size:98
Alignment explanation
Indices: 266395--266586 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 98
266385 CTGGAACTGG
* * * * *
266395 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCACCATGAAGTTGAGCTTATGCTGTCTTGAGTCT
1 GAAATTGTTTGTTGACAATCAGCCACCCCTTCACCATGAAGTTGAACTTATGCTATCTTGAGTCC
* *
266460 AATATCCTTCATTGTGAAGTTGAAATTGACTCT
66 AATATCCTTCACTGTAAAGTTGAAATTGACTCT
* * * * * *
266493 GAAAGTTGTTTGTTGATAATCAGCCATCCCTTCGCTATGAAGTTGAACTTGTGTTATCTTGAGTC
1 GAAA-TTGTTTGTTGACAATCAGCCACCCCTTCACCATGAAGTTGAACTTATGCTATCTTGAGTC
*
266558 CAATATCCTTCGCTGTAAAGTTGAAATTG
65 CAATATCCTTCACTGTAAAGTTGAAATTG
266587 GCATGATATC
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
98 4 0.05
99 75 0.95
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (98 bp):
GAAATTGTTTGTTGACAATCAGCCACCCCTTCACCATGAAGTTGAACTTATGCTATCTTGAGTCC
AATATCCTTCACTGTAAAGTTGAAATTGACTCT
Found at i:267681 original size:15 final size:17
Alignment explanation
Indices: 267661--267698 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
267651 TTGAACCCAC
267661 CTTTTTT-TTCT-TTCT
1 CTTTTTTCTTCTGTTCT
*
267676 CTTTTTTCTTTTGTTCT
1 CTTTTTTCTTCTGTTCT
267693 CTTTTT
1 CTTTTT
267699 CAATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 3 0.15
17 10 0.50
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
CTTTTTTCTTCTGTTCT
Found at i:267780 original size:81 final size:85
Alignment explanation
Indices: 267662--267822 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 85
267652 TGAACCCACC
* * * **
267662 TTTTTTTTCTTTCTCTTTTTTCTTTTGTTCTCTTTTTCAATTTTTTCAATTTAGGGCTTCCTTTC
1 TTTTTTTTCTTTCTCTTTGTTCTTTTGTTCTCTTTTTCAATTTTTTCAACTTAGGACGCCCTTTC
267727 GGGTTTTCACCCTAAAAGTT
66 GGGTTTTCACCCTAAAAGTT
** **
267747 TTTTTTTTCTTT-T-TTTGTTCTTTT-TTC-CTTTTTCCTTTTTTTTGACTTAGGACGCCCTTTC
1 TTTTTTTTCTTTCTCTTTGTTCTTTTGTTCTCTTTTTCAATTTTTTCAACTTAGGACGCCCTTTC
*
267808 GGGTTTTCATCCTAA
66 GGGTTTTCACCCTAA
267823 GCGAAGTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
81 40 0.61
82 3 0.05
83 10 0.15
84 1 0.02
85 12 0.18
ACGTcount: A:0.10, C:0.19, G:0.10, T:0.61
Consensus pattern (85 bp):
TTTTTTTTCTTTCTCTTTGTTCTTTTGTTCTCTTTTTCAATTTTTTCAACTTAGGACGCCCTTTC
GGGTTTTCACCCTAAAAGTT
Found at i:267788 original size:18 final size:18
Alignment explanation
Indices: 267746--267789 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
267736 CCCTAAAAGT
* **
267746 TTTTTTTTTCTTTTTTTG
1 TTTTTTTTTCCTTTTTCC
*
267764 TTCTTTTTTCCTTTTTCC
1 TTTTTTTTTCCTTTTTCC
267782 TTTTTTTT
1 TTTTTTTT
267790 GACTTAGGAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTCCTTTTTCC
Found at i:277448 original size:24 final size:24
Alignment explanation
Indices: 277421--277475 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
277411 TAAATTCACA
*
277421 CGAATGCATAAGGTATATGAATCC
1 CGAAGGCATAAGGTATATGAATCC
277445 CGAAGGCATAAGGTATATGAATCC
1 CGAAGGCATAAGGTATATGAATCC
277469 CGAAGGC
1 CGAAGGC
277476 TACTTGCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (24 bp):
CGAAGGCATAAGGTATATGAATCC
Found at i:278425 original size:27 final size:24
Alignment explanation
Indices: 278387--278444 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 24
278377 TAATAACAAT
*
278387 TATAATGATAATTATAAAAATATAAA
1 TATAATGATAA-TAGAAAAA-ATAAA
*
278413 TATATATGTTAATAGAAAAAATAAA
1 TATA-ATGATAATAGAAAAAATAAA
278438 TAGTAAT
1 TA-TAAT
278445 AATACTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 9 0.32
26 13 0.46
27 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (24 bp):
TATAATGATAATAGAAAAAATAAA
Found at i:278533 original size:26 final size:24
Alignment explanation
Indices: 278496--278554 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
278486 TAAACAAGGT
*
278496 ATAAA-AATAAAAGTAATAATAAGTA
1 ATAAATAA-AAAAATAATAAT-AGTA
*
278521 TTAAAATAAAAAAATAATAATAGTA
1 AT-AAATAAAAAAATAATAATAGTA
278546 ATAAATAAA
1 ATAAATAAA
278555 GTATAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 7 0.24
25 6 0.21
26 14 0.48
27 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (24 bp):
ATAAATAAAAAAATAATAATAGTA
Found at i:278540 original size:23 final size:24
Alignment explanation
Indices: 278494--278554 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
278484 TATAAACAAG
*
278494 GTATAAAAATAAAAGTAATAATAA
1 GTATAAAAATAAAAGAAATAATAA
*
278518 GTATTAAAATAAAA-AAATAATAA
1 GTATAAAAATAAAAGAAATAATAA
278541 -TAGTAATAAATAAA
1 GTA-TAA-AAATAAA
278555 GTATAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 10 0.31
24 20 0.62
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (24 bp):
GTATAAAAATAAAAGAAATAATAA
Found at i:278548 original size:20 final size:21
Alignment explanation
Indices: 278500--278590 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 21
278490 CAAGGTATAA
* *
278500 AAATAAAAGTAATAATAAGTATTA
1 AAATAAAA-AAATAATAA-TA-TG
278524 AAATAAAAAAATAATAATA-G
1 AAATAAAAAAATAATAATATG
* *
278544 TAATAAATAAAGT-ATAA-ATG
1 AAATAAA-AAAATAATAATATG
278564 AAAT-AAAAAATAATAATAATGG
1 AAATAAAAAAATAATAAT-AT-G
278586 AAATA
1 AAATA
278591 TAAGTAAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
18 4 0.07
19 7 0.13
20 14 0.26
21 6 0.11
22 7 0.13
23 8 0.15
24 8 0.15
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (21 bp):
AAATAAAAAAATAATAATATG
Found at i:278596 original size:39 final size:38
Alignment explanation
Indices: 278514--278596 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 38
278504 AAAAGTAATA
*
278514 ATAAGTATTAAAATAAAAAAATAATAATAGTAATAAAT
1 ATAAGTATTAAAATAAAAAAATAATAATAATAATAAAT
278552 A-AAGTA-T-AAATGAAATAAAA-AATAATAATAATGGAAAT
1 ATAAGTATTAAAAT-AAA-AAAATAATAATAATAAT--AAAT
278590 ATAAGTA
1 ATAAGTA
278597 AACATATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
35 4 0.10
36 15 0.38
37 9 0.23
38 6 0.15
39 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (38 bp):
ATAAGTATTAAAATAAAAAAATAATAATAATAATAAAT
Found at i:284022 original size:26 final size:27
Alignment explanation
Indices: 283993--284046 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
283983 ACGGTCTGAC
*
283993 GTGGCAG-TTTCTAGAAGGTCCAGTCA
1 GTGGCAGTTTTCTAGAAGATCCAGTCA
*
284019 GTGGCAGTTTTCTAGAAGATCTAGTCA
1 GTGGCAGTTTTCTAGAAGATCCAGTCA
284046 G
1 G
284047 CGCGCCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (27 bp):
GTGGCAGTTTTCTAGAAGATCCAGTCA
Found at i:285642 original size:3 final size:3
Alignment explanation
Indices: 285621--285659 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
285611 TCAAATAAAA
*
285621 AAC AAA AAC AA- AA- AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
285660 TAATAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:285778 original size:2 final size:2
Alignment explanation
Indices: 285773--285835 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
285763 AAAAATTGAA
285773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
285815 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
285836 AATGTAAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:290875 original size:43 final size:43
Alignment explanation
Indices: 290827--290919 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 43
290817 TAATCAACGA
*
290827 CGTTTGTCTCTAAAACGCTGCTATAGAAATTGACCTTTTGCGG
1 CGTTTGTCTCTAAAACACTGCTATAGAAATTGACCTTTTGCGG
* * * * * **
290870 CGTTTGTTTTTATAACATTGTTATAGATCTTGACCTTTTGCGG
1 CGTTTGTCTCTAAAACACTGCTATAGAAATTGACCTTTTGCGG
*
290913 TGTTTGT
1 CGTTTGT
290920 GATTAAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.44
Consensus pattern (43 bp):
CGTTTGTCTCTAAAACACTGCTATAGAAATTGACCTTTTGCGG
Found at i:294246 original size:28 final size:28
Alignment explanation
Indices: 294206--294264 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
294196 GGCTCATAGA
294206 TTAAACAAGCATAAATCAGGAAGTTTTC
1 TTAAACAAGCATAAATCAGGAAGTTTTC
294234 TTAAACAAGCATAAATCAGGAAGTTTTC
1 TTAAACAAGCATAAATCAGGAAGTTTTC
294262 TTA
1 TTA
294265 GTCTTTGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (28 bp):
TTAAACAAGCATAAATCAGGAAGTTTTC
Found at i:298141 original size:41 final size:41
Alignment explanation
Indices: 298074--298154 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
298064 ACCAAATGTG
298074 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
* *
298115 CTGAGCATTTATACACGAATGTACCAAAGCTGAACTGATA
1 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATA
298155 TGTACTCACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (41 bp):
CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
Found at i:301212 original size:13 final size:13
Alignment explanation
Indices: 301186--301228 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
301176 GGGTATCACA
301186 TTTTATTTCATTATT
1 TTTTATTT--TTATT
301201 TTTTATTTTTATT
1 TTTTATTTTTATT
* *
301214 TTTAATTTTAATT
1 TTTTATTTTTATT
301227 TT
1 TT
301229 GTAGGTACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 18 0.69
15 8 0.31
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:306550 original size:81 final size:81
Alignment explanation
Indices: 306410--306560 Score: 203
Period size: 81 Copynumber: 1.9 Consensus size: 81
306400 TATAATTCCT
* * * * * *
306410 TTATTCTTTTACCCAAAGGTATTTAGCCTTTAATCTAACTTGCATATTTGAAACTTTTCTGTCAA
1 TTATTCTTTTACCCAAAGATATTTAGCCGTTAATCTAACTGGCATAATTGAAACATTTCTGCCAA
306475 ATGCACAGCTAGTCTA
66 ATGCACAGCTAGTCTA
* * * * *
306491 TTATTCTTTTACTCAACGATATTTAGCCGTTCATCTAACTGGTATAATTGACACATTTCTGCCAA
1 TTATTCTTTTACCCAAAGATATTTAGCCGTTAATCTAACTGGCATAATTGAAACATTTCTGCCAA
306556 ATGCA
66 ATGCA
306561 TAGTTAGAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 59 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (81 bp):
TTATTCTTTTACCCAAAGATATTTAGCCGTTAATCTAACTGGCATAATTGAAACATTTCTGCCAA
ATGCACAGCTAGTCTA
Found at i:309713 original size:54 final size:54
Alignment explanation
Indices: 309653--309781 Score: 181
Period size: 54 Copynumber: 2.4 Consensus size: 54
309643 TATAAGGTAG
* * *
309653 TTCATCAACTCATGATGGA-TTCTGTGGGTTGCACACATCGTGTCTGTATGATTA
1 TTCATCAACTCATGATGAATTTCT-TGGGTTGCACACATCGTGCCTGTACGATTA
*
309707 TTCATCAACTCATGATGAATTTCTTGGGTTGCACACATCGTGCCTGTACGGTTA
1 TTCATCAACTCATGATGAATTTCTTGGGTTGCACACATCGTGCCTGTACGATTA
*
309761 TTCATCCACGT-ATGATGAATT
1 TTCATCAAC-TCATGATGAATT
309782 CCGTGAAATG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
54 63 0.93
55 5 0.07
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (54 bp):
TTCATCAACTCATGATGAATTTCTTGGGTTGCACACATCGTGCCTGTACGATTA
Found at i:309794 original size:54 final size:54
Alignment explanation
Indices: 309754--310182 Score: 633
Period size: 54 Copynumber: 7.9 Consensus size: 54
309744 TCGTGCCTGT
* *
309754 ACGGTTATTCATCCACGTATGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
309808 ACGGTTATTCATCCACGTAAGATGAATTCCGTGAATTGAACACTTAGTGCCGAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
309862 AAGGTTATTCATCCACGTAGGATGAATTCCATGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * * * * * * *
309916 ATGATTATTTATTCACGTAAGATGAATTCTGTGAAATGCACACTTAGTGTCAAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
309970 ACGGTTATTCATCCACGTAGGATAAATTCCGTGAAATGCACACTTAGTGTCAAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* **
310024 ACAGTTATTCATCCACGTAGGATGAATTCTATGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
310078 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
310132 ACGGTTATTCATCCACGTAAGATGAATTTCGTGAAATGTACACTTAGTGCC
1 ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCC
310183 TATTTGGTAA
Statistics
Matches: 338, Mismatches: 37, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 338 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (54 bp):
ACGGTTATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
Found at i:311582 original size:44 final size:44
Alignment explanation
Indices: 311509--311601 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
311499 GGAGTATCGG
* * * *
311509 TACCAGTATCGATATTGCAATGTATTTTTACACATTAGTATCAA
1 TACCAGTATCAATAATACAATGTAATTTTACACATTAGTATCAA
* *
311553 TACCAGTATCAATAATACAGTGTAATTTTACACATTAGTATCAG
1 TACCAGTATCAATAATACAATGTAATTTTACACATTAGTATCAA
311597 TACCA
1 TACCA
311602 AAATCAGTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (44 bp):
TACCAGTATCAATAATACAATGTAATTTTACACATTAGTATCAA
Found at i:318393 original size:6 final size:6
Alignment explanation
Indices: 318384--318408 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
318374 TACCCCATCC
318384 CCCATA CCCATA CCCATA CCCATA C
1 CCCATA CCCATA CCCATA CCCATA C
318409 TCACTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCATA
Found at i:318854 original size:15 final size:15
Alignment explanation
Indices: 318834--318864 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
318824 TAGTGAGTGA
*
318834 GCGGATGTGGGGCGG
1 GCGGATGCGGGGCGG
318849 GCGGATGCGGGGCGG
1 GCGGATGCGGGGCGG
318864 G
1 G
318865 TAAGGTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.68, T:0.10
Consensus pattern (15 bp):
GCGGATGCGGGGCGG
Found at i:319867 original size:15 final size:15
Alignment explanation
Indices: 319843--319877 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
319833 TCGTATCTAC
* *
319843 ATTTTGTTTGATTTG
1 ATTTTATTTGATTAG
319858 ATTTTATTTGATTAG
1 ATTTTATTTGATTAG
319873 ATTTT
1 ATTTT
319878 TTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (15 bp):
ATTTTATTTGATTAG
Found at i:320137 original size:21 final size:21
Alignment explanation
Indices: 320108--320180 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
320098 ATTCTGACTA
320108 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
320129 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
** * **
320150 TCGCAACGCGATTACGTAAA-
1 TCGCATTGCGATTTCCCAAAT
320170 TCGCATTGCGA
1 TCGCATTGCGA
320181 ATACGTAAAT
Statistics
Matches: 39, Mismatches: 13, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
20 9 0.23
21 30 0.77
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:320180 original size:20 final size:20
Alignment explanation
Indices: 320107--320194 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
320097 GATTCTGACT
* *
320107 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTACCTAA
* *
320127 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTACCTAA
* ** *
320149 TTCGCAACGCGATTACGTAA
1 ATCGCATTGCGATTACCTAA
* *
320169 ATCGCATTGCGAATACGTAA
1 ATCGCATTGCGATTACCTAA
320189 ATCGCA
1 ATCGCA
320195 ACGAGATTCT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 29 0.54
21 18 0.33
22 7 0.13
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGATTACCTAA
Found at i:323548 original size:20 final size:20
Alignment explanation
Indices: 323523--323570 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
323513 AGACATTAAT
*
323523 TTGACTATAGCAATGCGGAA
1 TTGACTATAGCAACGCGGAA
* *
323543 TTGACTATCGTAACGCGGAA
1 TTGACTATAGCAACGCGGAA
*
323563 ATGACTAT
1 TTGACTAT
323571 CACAACGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (20 bp):
TTGACTATAGCAACGCGGAA
Found at i:323577 original size:20 final size:20
Alignment explanation
Indices: 323524--323577 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
323514 GACATTAATT
* *
323524 TGACTAT-AGCAATGCGGAAT
1 TGACTATCA-CAACGCGGAAA
**
323544 TGACTATCGTAACGCGGAAA
1 TGACTATCACAACGCGGAAA
323564 TGACTATCACAACG
1 TGACTATCACAACG
323578 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TGACTATCACAACGCGGAAA
Found at i:323629 original size:52 final size:54
Alignment explanation
Indices: 323573--323683 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 54
323563 ATGACTATCA
323573 CAACGAGAGAATCGCAATGCG-AAATGAAAATCGCAATGCG-AAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGCGAAAATGAAAATCG
*
323625 CAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGCGAAAATGAAAATCG
323679 CAACG
1 CAACG
323684 CGAAATTAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 20 0.36
53 19 0.34
54 17 0.30
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (54 bp):
CAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGCGAAAATGAAAATCG
Found at i:323659 original size:20 final size:19
Alignment explanation
Indices: 323582--323689 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
323572 ACAACGAGAG
323582 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
323601 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
323620 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
323634 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
323654 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
323674 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
323690 TAGTTTCGCG
Statistics
Matches: 80, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
14 8 0.10
16 5 0.06
17 2 0.03
18 3 0.04
19 31 0.39
20 31 0.39
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:323756 original size:19 final size:19
Alignment explanation
Indices: 323693--323778 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
323683 GCGAAATTAG
323693 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
323712 TTTTCGCATTACGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
323730 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
323746 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
323765 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
323779 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.13
16 4 0.07
18 4 0.07
19 28 0.52
20 11 0.20
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:323899 original size:14 final size:15
Alignment explanation
Indices: 323880--323917 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
323870 CATCAATTAA
323880 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
323894 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
323908 ACAAATCAAT
1 ACAAATCAAT
323918 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:325308 original size:21 final size:21
Alignment explanation
Indices: 325284--325359 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
325274 GTGGGAGGGA
*
325284 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGAGG
* * *
325305 CCTCTTGAACGGTGAGAGAGG
1 CCTCTTCAACGATGACAGAGG
* * * * *
325326 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAACG-ATGACAGAGG
325347 CCTCTTCAACGAT
1 CCTCTTCAACGAT
325360 AGGAGTGGAC
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
20 3 0.08
21 32 0.82
22 4 0.10
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGAGG
Found at i:327336 original size:20 final size:20
Alignment explanation
Indices: 327311--327406 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
327301 TTTTGGTTGA
327311 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
327331 AATGAAAATCGCAACGCAGA-
1 AATGAAAATCGCAACG-AGAG
** *
327351 AATGACTATCGCAA--TGAG
1 AATGAAAATCGCAACGAGAG
*
327369 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
327384 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
327404 AAT
1 AAT
327407 CGCAACGCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 7 0.11
16 4 0.07
17 4 0.07
19 12 0.20
20 31 0.51
21 3 0.05
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:327395 original size:19 final size:19
Alignment explanation
Indices: 327309--327468 Score: 116
Period size: 19 Copynumber: 9.1 Consensus size: 19
327299 TCTTTTGGTT
*
327309 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
327328 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
327348 AGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
327366 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
327382 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
327399 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
327415 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
327432 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
327448 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
327467 GA
1 GA
327469 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
14 28 0.26
15 3 0.03
16 5 0.05
17 5 0.05
18 3 0.03
19 35 0.32
20 28 0.26
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:327395 original size:33 final size:33
Alignment explanation
Indices: 327309--327463 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 33
327299 TCTTTTGGTT
327309 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** *
327348 AGAAATGACTATCGCAATGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
327382 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
327415 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
327448 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
327464 TGCGATTTTG
Statistics
Matches: 107, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
33 77 0.72
34 11 0.10
36 1 0.01
37 1 0.01
38 3 0.03
40 14 0.13
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:327409 original size:14 final size:14
Alignment explanation
Indices: 327358--327446 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
327348 AGAAATGACT
*
327358 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
*
327372 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
327391 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
327405 ATCGCAACGCGAAATTAAA
1 ATCGCAA--CG--A-GAGA
327424 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
327438 ATCGCAACG
1 ATCGCAACG
327447 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 28 0.48
15 2 0.03
16 3 0.05
17 4 0.07
18 2 0.03
19 19 0.33
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:327514 original size:21 final size:20
Alignment explanation
Indices: 327495--327566 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
327485 CGATTCTCTC
327495 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
327515 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
327536 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
327556 GTTGCGATTTT
1 GTTGCGATTTT
327567 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:328155 original size:20 final size:20
Alignment explanation
Indices: 328130--328364 Score: 199
Period size: 20 Copynumber: 11.6 Consensus size: 20
328120 TTAAAAATCA
328130 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
328150 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
328170 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
* * * * *
328191 CATTGCGATTTATGTATTCT
1 CGTTGCGATTTACGGATACG
*
328211 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACG
* * *
328231 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
*
328251 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
* *
328271 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
*
328291 TCGTTGCGATTTACGGATATG
1 -CGTTGCGATTTACGGATACG
* * *
328312 CTTTGTGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
* *
328333 CATTGCGATAGTTA-GAAT-CG
1 CGTTGCGAT--TTACGGATACG
328353 CGTTGCGATTTA
1 CGTTGCGATTTA
328365 TATGTTCGCG
Statistics
Matches: 171, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.02
20 111 0.65
21 54 0.32
22 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:328339 original size:41 final size:41
Alignment explanation
Indices: 328130--328363 Score: 305
Period size: 41 Copynumber: 5.8 Consensus size: 41
328120 TTAAAAATCA
*
328130 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
328171 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
328211 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
328251 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * * *
328292 CGTTGCGATTTACGGATATGCTTTGTGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
328333 CATTGCGATAGTTA-GAAT-CGCGTTGCGATTT
1 CGTTGCGAT--TTACGGATACGCGTTGCGATTT
328364 ATATGTTCGC
Statistics
Matches: 169, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 73 0.43
41 90 0.53
42 3 0.02
43 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:328373 original size:20 final size:20
Alignment explanation
Indices: 328350--328402 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
328340 ATAGTTAGAA
*
328350 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
328370 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
328390 TCACGTTGCGATT
1 TCGCGTTGCGATT
328403 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:329397 original size:20 final size:21
Alignment explanation
Indices: 329358--329398 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
329348 TTATGAACTG
329358 CGTTTTCAAAACGTTTTTTTT
1 CGTTTTCAAAACGTTTTTTTT
329379 CGTTTTCAAAACGTTTTTTT
1 CGTTTTCAAAACGTTTTTTT
329399 GTTTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
CGTTTTCAAAACGTTTTTTTT
Found at i:329749 original size:37 final size:37
Alignment explanation
Indices: 329666--329737 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
329656 ATAAAAAATA
* *
329666 TAACATTTTTTTGTTGAACCGAAAATATTATGAAAAGG
1 TAACA-TTTTTTATTGAACCAAAAATATTATGAAAAGG
329704 TAACATTTTTTATTGAACCAAAAATATTA-GAAAA
1 TAACATTTTTTATTGAACCAAAAATATTATGAAAA
329738 TTTTAACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 5 0.16
37 22 0.69
38 5 0.16
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (37 bp):
TAACATTTTTTATTGAACCAAAAATATTATGAAAAGG
Found at i:333761 original size:30 final size:30
Alignment explanation
Indices: 333721--333779 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
333711 TTGCATCGTC
*
333721 TCATCCTTCACATATTCCTGTTACACCACT
1 TCATCCTTCACATAATCCTGTTACACCACT
* * * *
333751 TCATCTTTCACCTAATCTTGTTGCACCAC
1 TCATCCTTCACATAATCCTGTTACACCAC
333780 CTGATTCTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.36, G:0.05, T:0.37
Consensus pattern (30 bp):
TCATCCTTCACATAATCCTGTTACACCACT
Found at i:337160 original size:6 final size:6
Alignment explanation
Indices: 337152--337186 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
337142 TTTTATATTT
*
337152 TTTCCT TTTCCA TTTCCA TTTCCA TTTCCA TTTCC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCC
337187 CTAGGCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCCA
Found at i:338081 original size:18 final size:18
Alignment explanation
Indices: 338058--338093 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
338048 GGCATTTATG
338058 CCCTATGATCTGGGAACC
1 CCCTATGATCTGGGAACC
*
338076 CCCTATGATTTGGGAACC
1 CCCTATGATCTGGGAACC
338094 ACATCAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (18 bp):
CCCTATGATCTGGGAACC
Found at i:339302 original size:23 final size:23
Alignment explanation
Indices: 339251--339302 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
339241 GTTCGTTACA
*
339251 TATTTATGCTTTATTATTTTGTCC
1 TATTTATGATTTATTATTTTGT-C
339275 T-TTTATGATTTAGTTATTTTGT-
1 TATTTATGATTTA-TTATTTTGTC
339297 TATTTA
1 TATTTA
339303 ATGTCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 14 0.56
24 10 0.40
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (23 bp):
TATTTATGATTTATTATTTTGTC
Found at i:339361 original size:22 final size:22
Alignment explanation
Indices: 339336--339381 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
339326 AAACCGTTTA
339336 ATTAAATATGTTT-TTTTATGTT
1 ATTAAATAT-TTTATTTTATGTT
* *
339358 ATTAGATGTTTTATTTTATGTT
1 ATTAAATATTTTATTTTATGTT
339380 AT
1 AT
339382 ATTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (22 bp):
ATTAAATATTTTATTTTATGTT
Found at i:339463 original size:18 final size:19
Alignment explanation
Indices: 339436--339476 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
339426 TTATATGTTG
* *
339436 TTTATTTCATT-ATATTAT
1 TTTATCTCATTCATATTAA
339454 TTTATCTCATTCATATTAA
1 TTTATCTCATTCATATTAA
339473 TTTA
1 TTTA
339477 ATTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATCTCATTCATATTAA
Found at i:353092 original size:23 final size:22
Alignment explanation
Indices: 353066--353128 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
353056 TCAAAAGATA
353066 AAAAAATAAATAAAAATAGAGAG
1 AAAAAATAAATAAAAATAGA-AG
*
353089 AAAAAATAAA-AATAAATCGAAG
1 AAAAAATAAATAA-AAATAGAAG
*
353111 AAATAAATGAGATAAAAA
1 AAA-AAAT-AAATAAAAA
353129 ACAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 7 0.21
23 20 0.59
24 5 0.15
25 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAAAATAAATAAAAATAGAAG
Found at i:353117 original size:19 final size:19
Alignment explanation
Indices: 353052--353104 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
353042 AAAAAATAAT
353052 AAAATCAAAAGATAAA-A-AA
1 AAAAT-AAAA-ATAAAGAGAA
*
353071 ATAAATAAAAATAGAGAGAA
1 A-AAATAAAAATAAAGAGAA
353091 AAAATAAAAATAAA
1 AAAATAAAAATAAA
353105 TCGAAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.14
19 18 0.62
20 7 0.24
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAATAAAAATAAAGAGAA
Found at i:354273 original size:3 final size:3
Alignment explanation
Indices: 354265--354298 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
354255 AAAGTAAATA
354265 AAT AAT AAT AAT AAT AAAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
354299 TAGATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:354277 original size:13 final size:14
Alignment explanation
Indices: 354261--354312 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 14
354251 AATGAAAGTA
354261 AATAA-ATAATAAT
1 AATAATATAATAAT
354274 AATAATA-AATAAT
1 AATAATATAATAAT
354287 AATAATATAAT-AT
1 AATAATATAATAAT
*
354300 AGATTATATAATA
1 A-ATAATATAATA
354313 TATATTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 21 0.62
14 13 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:354282 original size:16 final size:16
Alignment explanation
Indices: 354261--354293 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
354251 AATGAAAGTA
354261 AATAAATAATAATAAT
1 AATAAATAATAATAAT
354277 AATAAATAATAATAAT
1 AATAAATAATAATAAT
354293 A
1 A
354294 TAATATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:354361 original size:27 final size:28
Alignment explanation
Indices: 354326--354378 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
354316 ATTTCAAAAA
*
354326 AAATATTTTTAAACTATATATTATATTT
1 AAATATTTTAAAACTATATATTATATTT
354354 AAAT-TTTTAAAACTATATATTATAT
1 AAATATTTTAAAACTATATATTATAT
354379 AGTTTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATATTTTAAAACTATATATTATATTT
Found at i:354421 original size:33 final size:31
Alignment explanation
Indices: 354370--354545 Score: 128
Period size: 33 Copynumber: 5.3 Consensus size: 31
354360 TTAAAACTAT
*
354370 ATATTATATAGTTTTCAAAAATGATTTTAAAA
1 ATATTATATAATTTTC-AAAATGATTTTAAAA
354402 ATATTATATAAGTTTTCAAAAAAT-ATTTTTTAAAACTA
1 ATATTATATAA-TTTTC--AAAATGA--TTTT-AAA--A
*
354440 TATATTATATAAATTTTTCAAAATGTTTTTAAAA
1 -ATATTATAT-AA-TTTTCAAAATGATTTTAAAA
*
354474 AT-TATATATTATATTTTCAAAATGATTTCAAAA
1 ATAT-TATA-TA-ATTTTCAAAATGATTTTAAAA
*
354507 GTA-TATATATATTTTCAAAATG-TTTTAAAA
1 ATATTATATA-ATTTTCAAAATGATTTTAAAA
354537 ACTA-TATAT
1 A-TATTATAT
354546 TATATATAAG
Statistics
Matches: 121, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
30 7 0.06
31 22 0.18
32 15 0.12
33 32 0.26
34 9 0.07
35 4 0.03
36 6 0.05
37 4 0.03
38 6 0.05
39 9 0.07
40 7 0.06
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (31 bp):
ATATTATATAATTTTCAAAATGATTTTAAAA
Found at i:354444 original size:34 final size:34
Alignment explanation
Indices: 354356--354545 Score: 132
Period size: 31 Copynumber: 5.5 Consensus size: 34
354346 TTATATTTAA
354356 ATTTTTAAAACTATATATTATATAGTTTTCAAAAATG
1 ATTTTTAAAAC--TATA-TATATAGTTTTCAAAAATG
*
354393 A-TTTTAAAAATAT-TATATAAGTTTTCAAAAAAT-
1 ATTTTTAAAACTATATATAT-AGTTTTC-AAAAATG
*
354426 ATTTTTTAAAACTATATATTATATAAATTTTTC-AAAATG
1 A-TTTTTAAAAC--TATA-TATAT--AGTTTTCAAAAATG
*
354465 -TTTTTAAAAATTATATATTATA-TTTTC-AAAATG
1 ATTTTT-AAAACTATATA-TATAGTTTTCAAAAATG
* *
354498 A-TTTCAAAAGTATATATATA-TTTTC-AAAATG
1 ATTTTTAAAACTATATATATAGTTTTCAAAAATG
*
354529 -TTTTAAAAACTATATAT
1 ATTTTTAAAACTATATAT
354546 TATATATAAG
Statistics
Matches: 131, Mismatches: 8, Indels: 34
0.76 0.05 0.20
Matches are distributed among these distances:
31 29 0.22
32 15 0.11
33 22 0.17
34 10 0.08
35 10 0.08
36 15 0.11
37 9 0.07
38 9 0.07
39 5 0.04
40 7 0.05
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (34 bp):
ATTTTTAAAACTATATATATAGTTTTCAAAAATG
Found at i:354478 original size:31 final size:31
Alignment explanation
Indices: 354354--354649 Score: 147
Period size: 36 Copynumber: 8.8 Consensus size: 31
354344 TATTATATTT
*
354354 AAAT-TTTTAAAACTATATATTATATAGTTTTCAA
1 AAATGTTTTAAAAAT-TATA-TATATA-TTTTC-A
354388 AAATGATTTTAAAAA-TAT-TATATAAGTTTTCAAAA
1 AAATG-TTTTAAAAATTATATATAT-A-TTTTC---A
* *
354423 AATATTTTTTAAAACTATATATTATATAAATTTTTCA
1 AA-ATGTTTTAAAA--AT-TA-TATATATA-TTTTCA
354460 AAATGTTTTTAAAAATTATATATTATATTTTCA
1 AAATG-TTTTAAAAATTATATA-TATATTTTCA
* * *
354493 AAATGATTTCAAAAGTATATATATATTTTCA
1 AAATGTTTTAAAAATTATATATATATTTTCA
* *
354524 AAATGTTTTAAAAACTATATAT-TA-TAT-A
1 AAATGTTTTAAAAATTATATATATATTTTCA
* *
354552 TAA-GTTTTCAAAAACTATATAATATATTTTCGAA
1 AAATGTTTT-AAAAATTATAT-ATATATTTTC--A
* * *
354586 AACCATTTTTTGAAAACTATATATTATATTTTTCAA
1 AA--ATGTTTTAAAAATTATATA-TATA-TTTTC-A
**
354622 AAACATTTTCAAAAATTATACTATATAT
1 AAATGTTTT-AAAAATTATA-TATATAT
354650 ATATATATAT
Statistics
Matches: 212, Mismatches: 22, Indels: 56
0.73 0.08 0.19
Matches are distributed among these distances:
27 5 0.02
28 14 0.07
29 4 0.02
30 4 0.02
31 31 0.15
32 18 0.08
33 22 0.10
34 20 0.09
35 27 0.13
36 33 0.16
37 21 0.10
39 2 0.01
40 7 0.03
41 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (31 bp):
AAATGTTTTAAAAATTATATATATATTTTCA
Found at i:354480 original size:38 final size:35
Alignment explanation
Indices: 354354--354551 Score: 161
Period size: 34 Copynumber: 5.8 Consensus size: 35
354344 TATTATATTT
*
354354 AAAT-TTTT-AAAACTATATATTATATAGTTTTCAA
1 AAATGTTTTAAAAACTATATATTATATAATTTTC-A
*
354388 AAATGATTTTAAAAA-TAT-TA-TATA-AGTTTTCAAA
1 AAATG-TTTTAAAAACTATATATTATATAATTTTC--A
* *
354422 AAATATTTTTTAAAACTATATATTATATAAATTTTTCA
1 AAAT-GTTTTAAAAACTATATATTATAT-AA-TTTTCA
*
354460 AAATGTTTTTAAAAATTATATA-T-TAT-ATTTTCA
1 AAATG-TTTTAAAAACTATATATTATATAATTTTCA
* * *
354493 AAATGATTTCAAAA--GTATA-TATAT-ATTTTCA
1 AAATGTTTTAAAAACTATATATTATATAATTTTCA
354524 AAATGTTTTAAAAACTATATATTATATA
1 AAATGTTTTAAAAACTATATATTATATA
354552 TAAGTTTTCA
Statistics
Matches: 135, Mismatches: 12, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
30 5 0.04
31 22 0.16
32 7 0.05
33 22 0.16
34 28 0.21
35 5 0.04
36 12 0.09
37 9 0.07
38 19 0.14
39 1 0.01
40 5 0.04
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (35 bp):
AAATGTTTTAAAAACTATATATTATATAATTTTCA
Found at i:354577 original size:26 final size:26
Alignment explanation
Indices: 354528--354578 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
354518 TTTTCAAAAT
354528 GTTTTAAAAACTATATATTATATATAA
1 GTTTTAAAAACTATATA-TATATATAA
354555 GTTTTCAAAAACTATATA-ATATAT
1 GTTTT-AAAAACTATATATATATAT
354579 TTTCGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.26
27 5 0.22
28 12 0.52
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
GTTTTAAAAACTATATATATATATAA
Found at i:354603 original size:64 final size:58
Alignment explanation
Indices: 354445--354614 Score: 162
Period size: 64 Copynumber: 2.7 Consensus size: 58
354435 AACTATATAT
* * * * *
354445 TATATAAAT-TTTTCAAAATGTTTTTAAAAATTATATATTATATTTTCAAAATGATTTCAAAAG
1 TATATATATATTTTCAAAATG-TTTTAAAAACTATATATTATA---T-ATAA-GTTTTCAAAAC
354508 TATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAAC
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATAAGTTTTC-AAAAC
* *
354567 TATATAATATATTTTCGAAAACCATTTTTTGAAAACTATATATTATAT
1 TATAT-ATATATTTTC--AAA--ATGTTTTAAAAACTATATATTATAT
354615 TTTTCAAAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
58 5 0.05
59 12 0.13
60 11 0.12
62 3 0.03
63 28 0.30
64 34 0.37
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (58 bp):
TATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAC
Found at i:365131 original size:22 final size:22
Alignment explanation
Indices: 365103--365148 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
365093 ATGGAGTGTT
365103 AATGCT-GAATTTTAATATTAGA
1 AATGCTGGAATTTTAA-ATTAGA
*
365125 AATGCTGGAATTTTAAGTTAGA
1 AATGCTGGAATTTTAAATTAGA
365147 AA
1 AA
365149 GTTTATTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (22 bp):
AATGCTGGAATTTTAAATTAGA
Found at i:366844 original size:44 final size:45
Alignment explanation
Indices: 366725--366849 Score: 162
Period size: 47 Copynumber: 2.8 Consensus size: 45
366715 ATAAAATCCT
* *
366725 TTACCATTTATCCCATAAGCTCGTAAGCTTATTCTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
366770 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
366817 TTGCTA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
366850 GTATGCTTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 24 0.34
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:367048 original size:59 final size:59
Alignment explanation
Indices: 366956--367084 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
366946 CGTAGTGCTA
* * **
366956 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
367015 TCCCGAATATGATACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
367074 TCCCGAATATG
1 TCCCGAATATG
367085 CAGCCTACTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:374316 original size:44 final size:45
Alignment explanation
Indices: 374197--374321 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 45
374187 ATAAAATCCT
* *
374197 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTGCCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * **
374242 TTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTACCCATGTAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
374289 TTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
374322 GTATGCTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 23 0.33
45 9 0.13
46 2 0.03
47 35 0.51
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:374522 original size:59 final size:59
Alignment explanation
Indices: 374430--374558 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
374420 CGTAGTGCTA
* * **
374430 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
374489 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
374548 TCCCGAATATG
1 TCCCGAATATG
374559 CAGCCTACTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:376619 original size:12 final size:12
Alignment explanation
Indices: 376602--376626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
376592 TTGTAAACAC
376602 ACATGACGTTGG
1 ACATGACGTTGG
376614 ACATGACGTTGG
1 ACATGACGTTGG
376626 A
1 A
376627 GAACCATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:378682 original size:21 final size:23
Alignment explanation
Indices: 378658--378712 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
378648 CCCCTTGCTA
378658 TGTATCGATACA-T-CTTGAATG
1 TGTATCGATACATTCCTTGAATG
* *
378679 TGTACCGATAGATTCCTTGAATG
1 TGTATCGATACATTCCTTGAATG
378702 TGTATCGATAC
1 TGTATCGATAC
378713 TCCCTGAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.36
22 1 0.04
23 17 0.61
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (23 bp):
TGTATCGATACATTCCTTGAATG
Found at i:383926 original size:48 final size:48
Alignment explanation
Indices: 383874--383969 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
383864 GGCAAAAAAA
383874 TAATGGCCTAATTTTGTTTGAAATACTTGCAACTCCATTTTCCAGCAC
1 TAATGGCCTAATTTTGTTTGAAATACTTGCAACTCCATTTTCCAGCAC
383922 TAATGGCCTAATTTTGTTTGAAATACTTGCAACTCCATTTTCCAGCAC
1 TAATGGCCTAATTTTGTTTGAAATACTTGCAACTCCATTTTCCAGCAC
383970 CAATTTCCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (48 bp):
TAATGGCCTAATTTTGTTTGAAATACTTGCAACTCCATTTTCCAGCAC
Found at i:384143 original size:9 final size:9
Alignment explanation
Indices: 384129--384180 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
384119 AGTTTGAGGA
384129 TTTTTTTATT
1 TTTTTTTA-T
*
384139 TTTTTTTTT
1 TTTTTTTAT
384148 TTTTTTTCAT
1 TTTTTTT-AT
*
384158 TTTTTTCCAT
1 TTTTTT-TAT
*
384168 TTTTTTCAT
1 TTTTTTTAT
384177 TTTT
1 TTTT
384181 CATTTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 15 0.41
10 22 0.59
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:384144 original size:10 final size:10
Alignment explanation
Indices: 384129--384173 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
384119 AGTTTGAGGA
384129 TTTTTTTATT
1 TTTTTTTATT
384139 TTTTTTT-TT
1 TTTTTTTATT
384148 TTTTTTTCATT
1 TTTTTTT-ATT
**
384159 TTTTTCCATT
1 TTTTTTTATT
384169 TTTTT
1 TTTTT
384174 CATTTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 9 0.29
10 15 0.48
11 7 0.23
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:384174 original size:10 final size:9
Alignment explanation
Indices: 384148--384180 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
384138 TTTTTTTTTT
384148 TTTTTTTCA
1 TTTTTTTCA
384157 TTTTTTTCCA
1 TTTTTTT-CA
384167 TTTTTTTCA
1 TTTTTTTCA
384176 TTTTT
1 TTTTT
384181 CATTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:385931 original size:20 final size:20
Alignment explanation
Indices: 385906--385962 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
385896 TACTTAACCC
385906 TAGAGTATCGATACTACAAG
1 TAGAGTATCGATACTACAAG
385926 TAGAGTATCGATACTACAAG
1 TAGAGTATCGATACTACAAG
*
385946 TAGAGTATCTATACTAC
1 TAGAGTATCGATACTAC
385963 TCACATTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (20 bp):
TAGAGTATCGATACTACAAG
Found at i:387627 original size:19 final size:19
Alignment explanation
Indices: 387605--387672 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 19
387595 GTTTTATAAA
387605 TGATATTTATGTTTATCAT
1 TGATATTTATGTTTATCAT
* *
387624 TGATACCATATAATATGTTTTATAAA
1 TGAT---AT-T--TATG-TTTATCAT
387650 TGATATTTATGTTTATCAT
1 TGATATTTATGTTTATCAT
387669 TGAT
1 TGAT
387673 TGAGTGTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 14 0.37
20 4 0.11
22 3 0.08
23 3 0.08
25 4 0.11
26 10 0.26
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.51
Consensus pattern (19 bp):
TGATATTTATGTTTATCAT
Found at i:387642 original size:45 final size:45
Alignment explanation
Indices: 387587--387672 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
387577 AGCTTCAATT
387587 TATAAAATGTTTTATAAATGATATTTATGTTTATCATTGATACCA
1 TATAAAATGTTTTATAAATGATATTTATGTTTATCATTGATACCA
*
387632 TATAATATGTTTTATAAATGATATTTATGTTTATCATTGAT
1 TATAAAATGTTTTATAAATGATATTTATGTTTATCATTGAT
387673 TGAGTGTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (45 bp):
TATAAAATGTTTTATAAATGATATTTATGTTTATCATTGATACCA
Found at i:387910 original size:29 final size:29
Alignment explanation
Indices: 387838--387911 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
387828 TCCGTAGAGG
* *
387838 ATCTCACACAGAATCAGGACAGGGATATA
1 ATCTCATACAGAATCAGGACAGAGATATA
* * * *
387867 ATCCCATGCAGAATCAGGATAGAGATATC
1 ATCTCATACAGAATCAGGACAGAGATATA
*
387896 ATCTCATACAAAATCA
1 ATCTCATACAGAATCA
387912 TGAATGCAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (29 bp):
ATCTCATACAGAATCAGGACAGAGATATA
Found at i:388091 original size:75 final size:75
Alignment explanation
Indices: 387968--388111 Score: 270
Period size: 75 Copynumber: 1.9 Consensus size: 75
387958 AATCAACCAG
387968 AATACGTACAAATAATATCATACATCATAACATCATAAAATATTAACAGTGTCAAACGGGTAAAA
1 AATACGTACAAATAATATCATACATCATAACATCATAAAATATTAACAGTGTCAAACGGGTAAAA
388033 GGGAAGCCAA
66 GGGAAGCCAA
* *
388043 AATACGTACAGATAATATCATACATCATAACATCATAAAATATTAACAGTGTCAAATGGGTAAAA
1 AATACGTACAAATAATATCATACATCATAACATCATAAAATATTAACAGTGTCAAACGGGTAAAA
388108 GGGA
66 GGGA
388112 TACACCTATT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (75 bp):
AATACGTACAAATAATATCATACATCATAACATCATAAAATATTAACAGTGTCAAACGGGTAAAA
GGGAAGCCAA
Found at i:390455 original size:19 final size:19
Alignment explanation
Indices: 390431--390535 Score: 120
Period size: 19 Copynumber: 5.2 Consensus size: 19
390421 GCGATTTTGA
390431 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
390450 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
390469 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
390489 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
390513 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
390532 AAAA
1 AAAA
390536 ATCCAAAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
19 52 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.13
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:390983 original size:20 final size:20
Alignment explanation
Indices: 390958--391070 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
390948 ATTTTGTATT
390958 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
390978 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
390998 TTCGCATTGCGA-A-TCTGGA
1 ATCGCGTTGCGATAGTC-AGA
* ** * *
391017 AACTGATTTGCGATACT-GGA
1 ATC-GCGTTGCGATAGTCAGA
391037 GATCGCGTTGCGATAGTCAGA
1 -ATCGCGTTGCGATAGTCAGA
391058 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
391071 TTACATATTC
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 59 0.84
21 5 0.07
22 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:391068 original size:40 final size:39
Alignment explanation
Indices: 390958--391090 Score: 99
Period size: 40 Copynumber: 3.3 Consensus size: 39
390948 ATTTTGTATT
* *
390958 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACAT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCTACAG
* * * ** **
390997 ATTCGCATTGCGA-A-TCTGGAAACTGATTTGCGATACTGGAG
1 A-TCGCGTTGCGATAGTC-AGAATC-GCGTTGCGAT-CTACAG
* *
391038 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACAT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCTACAG
*
391077 ATTCGCATTGCGAT
1 A-TCGCGTTGCGAT
391091 TTTCTAAAAT
Statistics
Matches: 68, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
38 2 0.03
39 9 0.13
40 47 0.69
41 8 0.12
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (39 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCTACAG
Found at i:394581 original size:30 final size:30
Alignment explanation
Indices: 394430--394612 Score: 129
Period size: 30 Copynumber: 6.1 Consensus size: 30
394420 GAATGGGAAC
* * * *
394430 AACATAAAATTAAATGACCAAAATAGTACA
1 AACATAAAATTAAAGGACTAAAATAGCAAA
* * *
394460 AACATGAACTTAATGGACTAAAATAG-AAA
1 AACATAAAATTAAAGGACTAAAATAGCAAA
* *
394489 AA-ATAGACATTTAAAGGACTAAAATAGAAAAA
1 AACATA-A-AATTAAAGGACTAAAATAG-CAAA
* * ** *
394521 AACATAAAATTAAGGGAATAAAGCAACAAA
1 AACATAAAATTAAAGGACTAAAATAGCAAA
* *
394551 AACATAAATTTAAAGGACTACAATAGCAAA
1 AACATAAAATTAAAGGACTAAAATAGCAAA
* * * *
394581 AATAGAAACTCAAA-GAGCTAAAATAGCAAA
1 AACATAAAATTAAAGGA-CTAAAATAGCAAA
394611 AA
1 AA
394613 TGGAAATTTA
Statistics
Matches: 119, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
28 2 0.02
29 7 0.06
30 88 0.74
31 13 0.11
32 6 0.05
33 3 0.03
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (30 bp):
AACATAAAATTAAAGGACTAAAATAGCAAA
Found at i:394632 original size:30 final size:30
Alignment explanation
Indices: 394475--394632 Score: 111
Period size: 30 Copynumber: 5.2 Consensus size: 30
394465 GAACTTAATG
* * *
394475 GACTAAAATAGAAAAAATAGACATTTAAAG
1 GACTAAAATAGCAAAAATAGAAATTTAAAA
* * * * **
394505 GACTAAAATAGAAAAAAACATAAAATTAAGG
1 GACTAAAATAG-CAAAAATAGAAATTTAAAA
* ** * * * *
394536 GAATAAAGCAACAAAAACATAAATTTAAAG
1 GACTAAAATAGCAAAAATAGAAATTTAAAA
* * *
394566 GACTACAATAGCAAAAATAGAAA-CTCAAA
1 GACTAAAATAGCAAAAATAGAAATTTAAAA
*
394595 GAGCTAAAATAGCAAAAATGGAAATTTAAAA
1 GA-CTAAAATAGCAAAAATAGAAATTTAAAA
394626 GACTAAA
1 GACTAAA
394633 CTGGTATTAA
Statistics
Matches: 99, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
29 5 0.05
30 67 0.68
31 27 0.27
ACGTcount: A:0.61, C:0.09, G:0.13, T:0.17
Consensus pattern (30 bp):
GACTAAAATAGCAAAAATAGAAATTTAAAA
Found at i:395951 original size:3 final size:3
Alignment explanation
Indices: 395930--396008 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
395920 CTGCAAAATG
* *
395930 TAA TAG TAA -AA TAAA TAA TAA TAA TAA TAA TAA -ATA CAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
*
395975 TAA TAA TAA TAA TAA TAA TAA TAA -AT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
396009 TTTTTGTATA
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
2 4 0.06
3 58 0.88
4 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:396499 original size:131 final size:131
Alignment explanation
Indices: 396260--396500 Score: 311
Period size: 131 Copynumber: 1.8 Consensus size: 131
396250 TCATACGTGG
* * * *
396260 TGAGAATGGCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATAAGAAGGTCTAGTCGGTGGAT
1 TGAGAATGGCTAGTTATCTAAGGGTGACACAGCTCCTACGTGATAAGAAGGTCTAGTCGGGGGAT
* * * *
396325 GACATGGTTTCTACGTAATGAGGATGATAGGACATCTTTAGGGATGATAACATAGTTCCTACATG
66 GACACGGTTCCTACGCAATGAGGATGACAGGACATCTTTAGGGATGATAACATAGTTCCTACATG
396390 A
131 A
* * * * * * *
396391 TGAGGATGGCTAGTTATTTAAGGTTGACACAGCTTCTACGTGATGAGGAGGTCTGGTCGGGGGAT
1 TGAGAATGGCTAGTTATCTAAGGGTGACACAGCTCCTACGTGATAAGAAGGTCTAGTCGGGGGAT
* * * *
396456 GACACGGTTCCTATGCGATGAGGATGACATGCCATCTTTAGGGAT
66 GACACGGTTCCTACGCAATGAGGATGACAGGACATCTTTAGGGAT
396501 AATGGTTTCA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
131 91 1.00
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (131 bp):
TGAGAATGGCTAGTTATCTAAGGGTGACACAGCTCCTACGTGATAAGAAGGTCTAGTCGGGGGAT
GACACGGTTCCTACGCAATGAGGATGACAGGACATCTTTAGGGATGATAACATAGTTCCTACATG
A
Found at i:396628 original size:66 final size:66
Alignment explanation
Indices: 396506--396681 Score: 196
Period size: 66 Copynumber: 2.6 Consensus size: 66
396496 GGGATAATGG
* * **
396506 TTTCAAGAGAAACCGA-CTCAAAGATGATGCTTCAAGAGAAGTTGTCTCAAGAGAGACAAAA-TT
1 TTTCAAGAGAAA-CGATCTCAAAGATGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
396569 TA
65 TA
* * *
396571 TTTCATGGGAAACGATCTCAAAGATGGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTT
1 TTTCAAGAGAAACGATCTCAAAGAT-GGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
396636 TG
65 TA
* *
396638 TTTCAAGAGAAAC-ATACTAAAAGATTTTGTGTTTCAAGAGAAAC
1 TTTCAAGAGAAACGAT-CTCAAAGA--TGGTGTTTCAAGAGAAAC
396682 AGACTCAAAG
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
64 3 0.03
65 19 0.20
66 33 0.35
67 21 0.23
68 16 0.17
69 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (66 bp):
TTTCAAGAGAAACGATCTCAAAGATGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTT
A
Found at i:396693 original size:98 final size:97
Alignment explanation
Indices: 396579--396759 Score: 258
Period size: 99 Copynumber: 1.9 Consensus size: 97
396569 TATTTCATGG
* *
396579 GAAACGATCTCAAAGA-TGGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCA
1 GAAACGATCTCAAAGATTGGGTGTTTCAAGAGAAACTGCCTCAAGGGAGACAAAA-TTTATTTCA
396643 AGAGAAACATACTAAAAGATTTTGTGTTTCAAGA
65 AGAGAAACA-ACTAAAAGATTTTGTGTTTCAAGA
** * *
396677 GAAACAGA-CTCAAAGATTTTGTGTTTCTAGATAAACTGCCTCAAGGGAGACAAAATTTATTTCA
1 GAAAC-GATCTCAAAGATTGGGTGTTTCAAGAGAAACTGCCTCAAGGGAGACAAAATTTATTTCA
*
396741 AGAGAAACAACTCAAAGAT
65 AGAGAAACAACTAAAAGAT
396760 GATTTTTTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
97 9 0.12
98 30 0.41
99 35 0.47
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (97 bp):
GAAACGATCTCAAAGATTGGGTGTTTCAAGAGAAACTGCCTCAAGGGAGACAAAATTTATTTCAA
GAGAAACAACTAAAAGATTTTGTGTTTCAAGA
Found at i:396720 original size:31 final size:31
Alignment explanation
Indices: 396636--396712 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
396626 GACAAAACTT
* *
396636 TGTTTCAAGAGAAACATACTAAAAGATTTTG
1 TGTTTCAAGAGAAACAGACTCAAAGATTTTG
396667 TGTTTCAAGAGAAACAGACTCAAAGATTTTG
1 TGTTTCAAGAGAAACAGACTCAAAGATTTTG
* *
396698 TGTTTCTAGATAAAC
1 TGTTTCAAGAGAAAC
396713 TGCCTCAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (31 bp):
TGTTTCAAGAGAAACAGACTCAAAGATTTTG
Found at i:396827 original size:100 final size:98
Alignment explanation
Indices: 396599--396830 Score: 247
Period size: 99 Copynumber: 2.3 Consensus size: 98
396589 CAAAGATGGG
* *
396599 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGAGAAACATACTAAAAGATT
1 TGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTATTTCAAGAGAAACATACTAAAAGATT
* *
396664 TTGTGTTTCAAGAGAAACAGACTCAAAGATTTTG
66 TTGTGTTTCAAGAGAAACAGACTC-AAGAATTTA
** * *
396698 TGTTTCTAGATAAACTGCCTCAAGGGAGACAAAA-TTTATTTCAAGAGAAACA-ACTCAAAGATG
1 TGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTATTTCAAGAGAAACATACT-AAA-A-G
* * * *
396761 ATTTTTTTGTTTCTAGTGAAACA-ATTTC-AGAATTTA
63 A-TTTTGTGTTTCAAGAGAAACAGA-CTCAAGAATTTA
* *
396797 TGTTTAAAGGGGAAACTGTCTCAAGCGAGACAAA
1 TGTTTAAA-GAGAAACTGTCTCAAGGGAGACAAA
396831 TCGGTTTTGA
Statistics
Matches: 111, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
97 3 0.03
98 20 0.18
99 44 0.40
100 24 0.22
101 20 0.18
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (98 bp):
TGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTATTTCAAGAGAAACATACTAAAAGATT
TTGTGTTTCAAGAGAAACAGACTCAAGAATTTA
Found at i:400480 original size:21 final size:21
Alignment explanation
Indices: 400441--400503 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
400431 CATATAAAAT
*
400441 TGTCCCGAATGACCACATATA
1 TGTCCCGAAGGACCACATATA
** *
400462 TGTCCCGAAGGACTGCATAGAA
1 TGTCCCGAAGGACCACATA-TA
*
400484 TTGTCCCTAAGGACCACATA
1 -TGTCCCGAAGGACCACATA
400504 GAACCCTCGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:400495 original size:23 final size:23
Alignment explanation
Indices: 400438--400506 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
400428 TGGCATATAA
*
400438 AATTGTCCCGAATGACCACATA-
1 AATTGTCCCGAAGGACCACATAG
* **
400460 TA-TGTCCCGAAGGACTGCATAG
1 AATTGTCCCGAAGGACCACATAG
*
400482 AATTGTCCCTAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
400505 AA
1 AA
400507 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 16 0.43
22 2 0.05
23 19 0.51
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:416737 original size:36 final size:32
Alignment explanation
Indices: 416667--416728 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
416657 AGAAAAAATG
416667 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
** *
416699 ACACAAACAAAAGAAGTGAAATCAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
416729 ACATGTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
Found at i:418617 original size:60 final size:61
Alignment explanation
Indices: 418544--418698 Score: 174
Period size: 60 Copynumber: 2.6 Consensus size: 61
418534 GAATGGAAAC
* * * * * *
418544 AACATAAACTTAAATGACTAAAATAGTACAAACAGGT-ACTTAAGGGACTAAAATAGA-AAA
1 AACAGAAATTTAAATGACTAAAATAGCAAAAACAGGTAACTTAAGGGAATAAAACA-ACAAA
* * *
418604 AACA-AACATTTAAAGGACTAAAATAGGAAAAATA-GTAACTTAAGGGAATAAAACAACAAA
1 AACAGAA-ATTTAAATGACTAAAATAGCAAAAACAGGTAACTTAAGGGAATAAAACAACAAA
*
418664 AACAGAAATTTAAATGACTACAATAGCAAAAACAG
1 AACAGAAATTTAAATGACTAAAATAGCAAAAACAG
418699 AAACTCAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
59 5 0.06
60 72 0.91
61 2 0.03
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (61 bp):
AACAGAAATTTAAATGACTAAAATAGCAAAAACAGGTAACTTAAGGGAATAAAACAACAAA
Found at i:418694 original size:30 final size:30
Alignment explanation
Indices: 418544--418730 Score: 137
Period size: 30 Copynumber: 6.3 Consensus size: 30
418534 GAATGGAAAC
* * * *
418544 AACATAAACTTAAATGACTAAAATAGTACA
1 AACAGAAACTTAAAGGACTAAAATAGCAAA
** * *
418574 AACAGGTACTTAAGGGACTAAAATAGAAAA
1 AACAGAAACTTAAAGGACTAAAATAGCAAA
* *
418604 AACA-AACATTTAAAGGACTAAAATAGGAAA
1 AACAGAA-ACTTAAAGGACTAAAATAGCAAA
* * * * * *
418634 AATAGTAACTTAAGGGAATAAAACAACAAA
1 AACAGAAACTTAAAGGACTAAAATAGCAAA
* * *
418664 AACAGAAATTTAAATGACTACAATAGCAAA
1 AACAGAAACTTAAAGGACTAAAATAGCAAA
* * *
418694 AACAGAAACTCAAAAGG-CTAAAACAGTAAA
1 AACAGAAACT-TAAAGGACTAAAATAGCAAA
418724 AAC-GAAA
1 AACAGAAA
418731 ATTTAAAAAA
Statistics
Matches: 119, Mismatches: 35, Indels: 7
0.74 0.22 0.04
Matches are distributed among these distances:
29 4 0.03
30 110 0.92
31 5 0.04
ACGTcount: A:0.58, C:0.12, G:0.13, T:0.17
Consensus pattern (30 bp):
AACAGAAACTTAAAGGACTAAAATAGCAAA
Found at i:420075 original size:18 final size:18
Alignment explanation
Indices: 420052--420099 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
420042 ATAGTAGATA
420052 AATAATAATAATACAAAT
1 AATAATAATAATACAAAT
420070 AATAATAATAATACAAAT
1 AATAATAATAATACAAAT
*
420088 AA-ATTAATAATA
1 AATAATAATAATA
420100 TTTTTGTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAATAATAATACAAAT
Found at i:420089 original size:15 final size:15
Alignment explanation
Indices: 420051--420079 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
420041 AATAGTAGAT
420051 AAATAATAATAATAC
1 AAATAATAATAATAC
420066 AAATAATAATAATA
1 AAATAATAATAATA
420080 ATACAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAATAATAATAC
Found at i:421365 original size:43 final size:43
Alignment explanation
Indices: 421167--421472 Score: 201
Period size: 44 Copynumber: 6.9 Consensus size: 43
421157 TCAATAATCA
** *
421167 ATTGAAAAACTTAGGGGAATCAATTATAAAGGTAGAAATTGAG
1 ATTGAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAG
* * *
421210 TTTGAAAAAGTTTAGAGGCCTCAATTATAAAGGTAGAAAGTGAG
1 ATTGAAAAA-CTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAG
* * * * *
421254 ATTGAAAAACTTAAGGGCCTCAACTATAAAGTTAAAAAAGTGGG
1 ATTGAAAAACTTAGGGGCCTCAATTATAAAGGT-AGAAAGTGAG
* * ** * * * *
421298 ATTAAAAAAATTAAAGGCTTCAATTATCAATGTAGAAATTGAG
1 ATTGAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAG
* *
421341 ATTGACAAAA-TTAGGGGCGTCAATTGTAAAGGTAGAAAATGTAGAAAGTGAG
1 ATTGA-AAAACTTAGGGGCCTCAA-T-T--A--T---AAAGGTAGAAAGTGAG
* * *
421393 ATTGAAAAAAC-TAAGGGCCTCAATTATAAAGTTA-ACAGGTGAG
1 ATTG-AAAAACTTAGGGGCCTCAATTATAAAGGTAGA-AAGTGAG
*
421436 ATT-ATAAAA-TTAAGGGCCT-AAGTTATAAAGGTAGAAA
1 ATTGA-AAAACTTAGGGGCCTCAA-TTATAAAGGTAGAAA
421473 ATGTAGAAAG
Statistics
Matches: 206, Mismatches: 38, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
41 3 0.01
42 25 0.12
43 63 0.31
44 75 0.36
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 32 0.16
53 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (43 bp):
ATTGAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAG
Found at i:421416 original size:52 final size:52
Alignment explanation
Indices: 421326--421527 Score: 201
Period size: 52 Copynumber: 4.1 Consensus size: 52
421316 TTCAATTATC
* * * * * *
421326 AATGTAGAAATTGAGATTGACAAAATTAGGGGCGTCAATTGTAAAGGTAGAA
1 AATGTAGAAAGTGAGATTGAAAAAACTAAGGGCCTCAATTATAAAGGTAGAA
*
421378 AATGTAGAAAGTGAGATTGAAAAAACTAAGGGCCTCAATTATAAA-GT---T
1 AATGTAGAAAGTGAGATTGAAAAAACTAAGGGCCTCAATTATAAAGGTAGAA
* * *
421426 AA--CAG---GTGAGATT-ATAAAATTAAGGGCCT-AAGTTATAAAGGTAGAA
1 AATGTAGAAAGTGAGATTGAAAAAACTAAGGGCCTCAA-TTATAAAGGTAGAA
* *
421472 AATGTAGAAAGTGAGATTGAAAAAACGTAAGGGCCTCAATTATAAAGTTAAAA
1 AATGTAGAAAGTGAGATTGAAAAAAC-TAAGGGCCTCAATTATAAAGGTAGAA
421525 AAT
1 AAT
421528 TGAATTAAAT
Statistics
Matches: 121, Mismatches: 16, Indels: 25
0.75 0.10 0.15
Matches are distributed among these distances:
41 2 0.02
42 21 0.17
43 10 0.08
46 4 0.03
48 4 0.03
51 10 0.08
52 44 0.36
53 24 0.20
54 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.24
Consensus pattern (52 bp):
AATGTAGAAAGTGAGATTGAAAAAACTAAGGGCCTCAATTATAAAGGTAGAA
Found at i:421416 original size:95 final size:94
Alignment explanation
Indices: 421337--421522 Score: 293
Period size: 94 Copynumber: 2.0 Consensus size: 94
421327 ATGTAGAAAT
* * *
421337 TGAGATTGACAAAATTAGGGGCGTCAA-TTGTAAAGGTAGAAAATGTAGAAAGTGAGATTGAAAA
1 TGAGATT-ACAAAATTAAGGGCCT-AAGTTATAAAGGTAGAAAATGTAGAAAGTGAGATTGAAAA
*
421401 AACTAAGGGCCTCAATTATAAAGTTAACAGG
64 AACTAAGGGCCTCAATTATAAAGTTAACAAG
*
421432 TGAGATTATAAAATTAAGGGCCTAAGTTATAAAGGTAGAAAATGTAGAAAGTGAGATTGAAAAAA
1 TGAGATTACAAAATTAAGGGCCTAAGTTATAAAGGTAGAAAATGTAGAAAGTGAGATTGAAAAAA
421497 CGTAAGGGCCTCAATTATAAAGTTAA
66 C-TAAGGGCCTCAATTATAAAGTTAA
421523 AAAATTGAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
93 2 0.02
94 52 0.61
95 31 0.36
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (94 bp):
TGAGATTACAAAATTAAGGGCCTAAGTTATAAAGGTAGAAAATGTAGAAAGTGAGATTGAAAAAA
CTAAGGGCCTCAATTATAAAGTTAACAAG
Done.